3KUU - JenaLib

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Biological Unit 6 (Jmol Viewer)

Title :   STRUCTURE OF THE PURE PHOSPHORIBOSYLAMINOIMIDAZOLE CARBOXYLASE CATALYTIC SUBUNIT FROM YERSINIA PESTIS

Authors :   S. M. Anderson, Z. Wawrzak, J. S. Brunzelle, O. Onopriyenko, K. Kwon, A. A. Savchenko, W. F. Anderson, Center For Structural Genomics Of Infectious Diseases (Csgid)

Date :   27 Nov 09 (Deposition) - 22 Dec 09 (Release) - 14 Dec 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.41

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: C  (1x)
Biol. Unit 4: D  (1x)
Biol. Unit 5: A,B  (4x)
Biol. Unit 6: C,D  (4x)

Keywords :   3-Layer (Aba) Sandwich, Rossmann Fold, Csgid, Lyase, Structural Genomics, Center For Structural Genomics Of Infectious Diseases (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. M. Anderson, Z. Wawrzak, J. S. Brunzelle, O. Onopriyenko, K. Kwon, A. Edwards, A. Savchenko, W. F. Anderson
Structure Of The Pure Phosphoribosylaminoimidazole Carboxylase Catalytic Subunit From Yersinia Pestis
To Be Published
PubMed: search

Molecule 1 - PHOSPHORIBOSYLAMINOIMIDAZOLE CARBOXYLASE CATALYTIC SUBUNIT PURE
	Chains	:	A, B, C, D
	EC Number	:	4.1.1.21
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21-CODONPLUS(DE3)-RIL
	Expression System Taxid	:	469008
	Gene	:	PURE, YPO3076, YP_0848, Y1103
	Mutation	:	YES
	Organism Scientific	:	YERSINIA PESTIS
	Organism Taxid	:	632
	Strain	:	CO92
	Synonym	:	PHOSPHORIBOSYLAMINOIMIDAZOLE CARBOXYLASE, CATALYTIC SUBUNIT

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B
Biological Unit 3 (1x)	:			C
Biological Unit 4 (1x)	:				D
Biological Unit 5 (4x)	:	A	B
Biological Unit 6 (4x)	:			C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 30)

No.	Name	Count	Type	Full Name
1	MSE	16	Mod. Amino Acid	SELENOMETHIONINE
2	SO4	14	Ligand/Ion	SULFATE ION

Biological Unit 1 (2, 8)

No.	Name	Count	Type	Full Name
1	MSE	4	Mod. Amino Acid	SELENOMETHIONINE
2	SO4	4	Ligand/Ion	SULFATE ION

Biological Unit 2 (2, 7)

No.	Name	Count	Type	Full Name
1	MSE	4	Mod. Amino Acid	SELENOMETHIONINE
2	SO4	3	Ligand/Ion	SULFATE ION

Biological Unit 3 (2, 10)

No.	Name	Count	Type	Full Name
1	MSE	4	Mod. Amino Acid	SELENOMETHIONINE
2	SO4	6	Ligand/Ion	SULFATE ION

Biological Unit 4 (2, 5)

No.	Name	Count	Type	Full Name
1	MSE	4	Mod. Amino Acid	SELENOMETHIONINE
2	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 5 (2, 60)

No.	Name	Count	Type	Full Name
1	MSE	32	Mod. Amino Acid	SELENOMETHIONINE
2	SO4	28	Ligand/Ion	SULFATE ION

Biological Unit 6 (2, 60)

No.	Name	Count	Type	Full Name
1	MSE	32	Mod. Amino Acid	SELENOMETHIONINE
2	SO4	28	Ligand/Ion	SULFATE ION

Asymmetric Unit (14, 14)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	GLN A:99 , GLY A:127 , LYS A:128 , HOH A:181 , HOH A:211 , HOH A:458 , HOH A:570	BINDING SITE FOR RESIDUE SO4 A 175
02	AC2	SOFTWARE	SER A:100 , ALA A:101 , HOH A:237 , HOH A:247 , HOH A:372 , HOH A:465 , HOH A:498 , HOH A:636	BINDING SITE FOR RESIDUE SO4 A 176
03	AC3	SOFTWARE	SER A:21 , LYS A:22 , SER A:23 , ARG A:51 , HOH A:657 , HOH A:747 , HOH A:818 , HOH A:859	BINDING SITE FOR RESIDUE SO4 A 177
04	AC4	SOFTWARE	HIS A:155 , HOH A:221 , HOH A:242 , HOH A:370 , ALA C:11 , HOH C:501	BINDING SITE FOR RESIDUE SO4 A 178
05	AC5	SOFTWARE	GLN B:99 , GLY B:127 , LYS B:128 , HOH B:195 , HOH B:860 , HOH B:861 , HOH B:873	BINDING SITE FOR RESIDUE SO4 B 175
06	AC6	SOFTWARE	SER B:100 , ALA B:101 , HOH B:229 , HOH B:293 , HOH B:408 , HOH B:419 , HOH B:456	BINDING SITE FOR RESIDUE SO4 B 176
07	AC7	SOFTWARE	SER B:21 , LYS B:22 , SER B:23 , ARG B:51 , HOH B:790 , HOH B:848 , HOH B:871	BINDING SITE FOR RESIDUE SO4 B 177
08	AC8	SOFTWARE	HOH C:197 , HOH C:261 , GLN D:99 , GLY D:127 , LYS D:128 , HOH D:193	BINDING SITE FOR RESIDUE SO4 C 175
09	AC9	SOFTWARE	GLN C:99 , GLY C:127 , LYS C:128 , HOH C:184 , HOH C:188 , HOH C:405 , HOH C:577	BINDING SITE FOR RESIDUE SO4 C 176
10	BC1	SOFTWARE	HOH C:221 , HOH C:317 , HOH C:383 , HOH C:686 , HOH C:710 , SER D:100 , ALA D:101 , HOH D:474	BINDING SITE FOR RESIDUE SO4 C 177
11	BC2	SOFTWARE	SER C:100 , ALA C:101 , HOH C:223 , HOH C:247 , HOH C:336 , HOH C:377 , HOH D:584	BINDING SITE FOR RESIDUE SO4 C 178
12	BC3	SOFTWARE	SER C:21 , LYS C:22 , SER C:23 , ARG C:51 , HOH C:673 , HOH C:704	BINDING SITE FOR RESIDUE SO4 C 179
13	BC4	SOFTWARE	LYS C:14 , HIS C:69 , HOH C:780 , HOH C:845	BINDING SITE FOR RESIDUE SO4 C 180
14	BC5	SOFTWARE	HIS D:43 , ASN D:66	BINDING SITE FOR RESIDUE SO4 D 175

(no "SS Bond" information available for 3KUU)

(no "Cis Peptide Bond" information available for 3KUU)

(no "SAP(SNP)/Variant" information available for 3KUU)

(no "PROSITE Motif" information available for 3KUU)

(no "Exon" information available for 3KUU)

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:169
 aligned with Q7CJZ1_YERPE | Q7CJZ1 from UniProtKB/TrEMBL  Length:174

    Alignment length:169
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165         
         Q7CJZ1_YERPE     6 NSAYAAGVKIAIVMGSKSDWATMQFAADVLTTLNVPFHVEVVSAHRTPDRLFSFAEQAEANGLHVIIAGAGGAAHLPGMLAAKTLVPVLGVPVQSAALSGVDSLYSIVQMPRGIPVGTLAIGKAGAANAALLAAQILALHDTELAGRLAHWRQSQTDDVLDNPDPREEA 174
               SCOP domains d3kuua_ A: automated matches                                                                                                                                              SCOP domains
               CATH domains 3kuuA00 A:6-174  [code=3.40.50.7700, no name defined]                                                                                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeeee.hhhhhhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhh......eeeeeee...hhhhhhhhh....eeeeee......hhhhhhhhhh.......ee...hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kuu A   6 NSAYAAGVKIAIVmGSKSDWATmQFAADVLTTLNVPFHVEVVSAHRTPDRLFSFAEQAEANGLHVIIAGNGGAAHLPGmLAAKTLVPVLGVPVQSAALSGVDSLYSIVQmPRGIPVGTLAIGKAGAANAALLAAQILALHDTELAGRLAHWRQSQTDDVLDNPDPREEA 174
                                    15   |    25  |     35        45        55        65        75        85        95       105       115       125       135       145       155       165         
                                        19-MSE   28-MSE                                                  84-MSE                        115-MSE

Chain B from PDB  Type:PROTEIN  Length:162
 aligned with Q7CJZ1_YERPE | Q7CJZ1 from UniProtKB/TrEMBL  Length:174

    Alignment length:162
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171  
         Q7CJZ1_YERPE    12 GVKIAIVMGSKSDWATMQFAADVLTTLNVPFHVEVVSAHRTPDRLFSFAEQAEANGLHVIIAGAGGAAHLPGMLAAKTLVPVLGVPVQSAALSGVDSLYSIVQMPRGIPVGTLAIGKAGAANAALLAAQILALHDTELAGRLAHWRQSQTDDVLDNPDPREE 173
               SCOP domains d3kuub_ B: automated matches                                                                                                                                       SCOP domains
               CATH domains 3kuuB00 B:12-173  [code=3.40.50.7700, no name defined]                                                                                                             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeee.hhhhhhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhh......eeeeee....hhhhhhhhhh...eeeee.......hhhhhhhhhh.......ee...hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3kuu B  12 GVKIAIVmGSKSDWATmQFAADVLTTLNVPFHVEVVSAHRTPDRLFSFAEQAEANGLHVIIAGNGGAAHLPGmLAAKTLVPVLGVPVQSAALSGVDSLYSIVQmPRGIPVGTLAIGKAGAANAALLAAQILALHDTELAGRLAHWRQSQTDDVLDNPDPREE 173
                                   |21      | 31        41        51        61        71        81  |     91       101       111   |   121       131       141       151       161       171  
                                  19-MSE   28-MSE                                                  84-MSE                        115-MSE

Chain C from PDB  Type:PROTEIN  Length:167
 aligned with Q7CJZ1_YERPE | Q7CJZ1 from UniProtKB/TrEMBL  Length:174

    Alignment length:167
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       
         Q7CJZ1_YERPE     8 AYAAGVKIAIVMGSKSDWATMQFAADVLTTLNVPFHVEVVSAHRTPDRLFSFAEQAEANGLHVIIAGAGGAAHLPGMLAAKTLVPVLGVPVQSAALSGVDSLYSIVQMPRGIPVGTLAIGKAGAANAALLAAQILALHDTELAGRLAHWRQSQTDDVLDNPDPREEA 174
               SCOP domains d3kuuc_ C: automated matches                                                                                                                                            SCOP domains
               CATH domains 3kuuC00 C:8-174  [code=3.40.50.7700, no name defined]                                                                                                                   CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhh..eeeee.hhhhhhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhh......eeeeee....hhhhhhhhhh...eeeee.......hhhhhhhhhh.......ee...hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kuu C   8 AYAAGVKIAIVmGSKSDWATmQFAADVLTTLNVPFHVEVVSAHRTPDRLFSFAEQAEANGLHVIIAGNGGAAHLPGmLAAKTLVPVLGVPVQSAALSGVDSLYSIVQmPRGIPVGTLAIGKAGAANAALLAAQILALHDTELAGRLAHWRQSQTDDVLDNPDPREEA 174
                                    17 |      27|       37        47        57        67        77      | 87        97       107       117       127       137       147       157       167       
                                      19-MSE   28-MSE                                                  84-MSE                        115-MSE

Chain D from PDB  Type:PROTEIN  Length:165
 aligned with Q7CJZ1_YERPE | Q7CJZ1 from UniProtKB/TrEMBL  Length:174

    Alignment length:165
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169     
         Q7CJZ1_YERPE    10 AAGVKIAIVMGSKSDWATMQFAADVLTTLNVPFHVEVVSAHRTPDRLFSFAEQAEANGLHVIIAGAGGAAHLPGMLAAKTLVPVLGVPVQSAALSGVDSLYSIVQMPRGIPVGTLAIGKAGAANAALLAAQILALHDTELAGRLAHWRQSQTDDVLDNPDPREEA 174
               SCOP domains d3kuud_ D: automated matches                                                                                                                                          SCOP domains
               CATH domains 3kuuD00 D:10-174  [code=3.40.50.7700, no name defined]                                                                                                                CATH domains
           Pfam domains (1) ---AIRC-3kuuD01 D:13-164                                                                                                                                   ---------- Pfam domains (1)
           Pfam domains (2) ---AIRC-3kuuD02 D:13-164                                                                                                                                   ---------- Pfam domains (2)
           Pfam domains (3) ---AIRC-3kuuD03 D:13-164                                                                                                                                   ---------- Pfam domains (3)
           Pfam domains (4) ---AIRC-3kuuD04 D:13-164                                                                                                                                   ---------- Pfam domains (4)
         Sec.struct. author .....eeeee.hhhhhhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhh......eeeeee....hhhhhhhhhh...eeeee.......hhhhhhhhhh.......ee...hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kuu D  10 AAGVKIAIVmGSKSDWATmQFAADVLTTLNVPFHVEVVSAHRTPDRLFSFAEQAEANGLHVIIAGNGGAAHLPGmLAAKTLVPVLGVPVQSAALSGVDSLYSIVQmPRGIPVGTLAIGKAGAANAALLAAQILALHDTELAGRLAHWRQSQTDDVLDNPDPREEA 174
                                    19        29        39        49        59        69        79    |   89        99       109     | 119       129       139       149       159       169     
                                    19-MSE   28-MSE                                                  84-MSE                        115-MSE

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: Flavodoxin-like (1057)

Superfamily: N5-CAIR mutase (phosphoribosylaminoimidazole carboxylase, PurE) (32)

Family: N5-CAIR mutase (phosphoribosylaminoimidazole carboxylase, PurE) (22)

Protein domain: automated matches (3)

Yersinia pestis [TaxId: 632] (1)

1a	d3kuua_	A:
1b	d3kuub_	B:
1c	d3kuuc_	C:
1d	d3kuud_	D:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: [code=3.40.50.7700, no name defined] (21)

Yersinia pestis. Organism_taxid: 632. Strain: co92. (1)

1a	3kuuD00	D:10-174
1b	3kuuB00	B:12-173
1c	3kuuC00	C:8-174
1d	3kuuA00	A:6-174

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: AIRC] (12)

Family: AIRC (12)

Yersinia pestis (1)

1a	AIRC-3kuuD01	D:13-164
1b	AIRC-3kuuD02	D:13-164
1c	AIRC-3kuuD03	D:13-164
1d	AIRC-3kuuD04	D:13-164

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (Q7CJZ1_YERPE | Q7CJZ1)

molecular function
	GO:0034023	5-(carboxyamino)imidazole ribonucleotide mutase activity	Catalysis of the reaction: 5-carboxyamino-1-(5-phospho-D-ribosyl)imidazole = 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate.
	GO:0016853	isomerase activity	Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
	GO:0016829	lyase activity	Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
biological process
	GO:0006189	'de novo' IMP biosynthetic process	The chemical reactions and pathways resulting in the formation of IMP, inosine monophosphate, by the stepwise assembly of a purine ring on ribose 5-phosphate.
	GO:0006164	purine nucleotide biosynthetic process	The chemical reactions and pathways resulting in the formation of a purine nucleotide, a compound consisting of nucleoside (a purine base linked to a deoxyribose or ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.

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Description

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Chains, Units

Ligands, Modified Residues, Ions (2, 30)

Sites (14, 14)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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